plotPromoters {proActiv} | R Documentation |
Visualizes promoter activity and transcript model for a gene of interest
plotPromoters( result, gene, txdb, ranges, cex.title = 0.9, cex.axis = 0.9, cex.main = 1, blk.width = 500, blk.fill = "grey", blk.border = "darkgrey", label.col = "black", label.size = 0.7, arrow.width = NULL, arrow.fill = "transparent", arrow.border = "grey" )
result |
A SummarizedExperiment object with assays giving promoter counts and activity with gene expression stored as column data and promoter gene id mapping stored as row data |
gene |
A character vector of length 1. Single gene of interest to be plotted |
txdb |
A TxDb object. The txdb must correspond to the genome version used in running proActiv. Here, it is recommended to use the same txdb in generating promoter annotations |
ranges |
A list of GRanges. Each entry in the list should correspond to a transcript that will be visualized, with Genomic Ranges giving the exons corresponding to that transcript |
cex.title |
A numeric value. Size of axis labels. Defaults to 0.9 |
cex.axis |
A numeric value. Size of axis and axis ticks. Defaults to 0.9 |
cex.main |
A numeric value. Size of plot name. Defaults to 1 |
blk.width |
A numeric value. The width of promoters blocks in the data track. Defaults to 500 (bases) |
blk.fill |
A character vector of length 1. The fill colour of the promoter blocks in the data track. Defaults to 'grey' |
blk.border |
A character vector of length 1. The border colour of the promoter blocks in the data track. Defaults to 'darkgrey' |
label.col |
A character vector of length 1. The font colour of the promoter ID label in the annotation track. Defaults to 'black' |
label.size |
A numeric value. The size of the promoter ID label in the annotation track. Defaults to 0.7 |
arrow.width |
A numeric value. The width of promoter arrows in the annotation track. This value is internally calculated based on the gene of interest |
arrow.fill |
A character vector of length 1. The fill colour of the promoter arrows in the annotation track. Defaults to 'transparent' |
arrow.border |
A character vector of length 1. The border colour of the promoter arrows in the annotation track. Defaults to 'grey' |
Outputs a plot of the promoters of the gene of interest across conditions, along with a model of transcripts belonging to the gene
## First, run proActiv to generate a summarizedExperiment result files <- list.files(system.file('extdata/vignette/junctions', package = 'proActiv'), full.names = TRUE) promoterAnnotation <- promoterAnnotation.gencode.v34.subset result <- proActiv(files = files, promoterAnnotation = promoterAnnotation, condition = rep(c('A549','HepG2'), each=3), ncores = 1) ## Read in pre-computed ranges txdb <- AnnotationDbi::loadDb(system.file('extdata/vignette/annotations', 'gencode.v34.annotation.rap1gap.sqlite', package = 'proActiv')) ## Declare a gene of interest gene <- 'ENSG00000076864.19' ## Call plot plotPromoters(result = result, gene = gene, txdb = txdb)